Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_588 | N | Molecule | Cyanocobalamin | 88 nM | 1 M LiCl, 5 mM MgC12, and 25 mM HEPES (pH 7.4) or 1 M NaCl, 5 mM MgC12, and 25 mM HEPES (pH 7.4) | 7508262 |
Structure information of aptamer
| Aptamer Sequence: | CCGGUGCGCAUAACCACCUCAGUGCGAGCAAGGAA |
| The optimal secondary structure in dot-bracket notation: | ((.((.(((((..........))))).))..)).. |
| The centroid secondary structure in dot-bracket notation: | ((.((.(((((..........))))).))..)).. |
The MFE structure
The Centroid structure
The mountain plot representation
Aptamer information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Aptamer ID | Apta_588 | Description | N |
| Aptamer chemistry | RNA | Length | 35 nt |
| GC content | 60.0% | Molecular weight | 11,263.81 Da |
| Molarity of 1 μg/μl solution | 88.78 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Aptasensor |
| Sequence | CCGGUGCGCAUAACCACCUCAGUGCGAGCAAGGAA | ||
| Applications | Recognition of cyanocobalamin | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| PubChem ID | 5311498 | Molecular name | Cyanocobalamin |
| Molecular formula | C63H88CoN14O14P | Molecular weight | 1355.4 |
| IUPAC name | cobalt(3+);[(2R,3S,4R,5S)-5-(5,6-dimethylbenzimidazol-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] [(2R)-1-[3-[(1R,2R,3R,5Z,7S,10Z,12S,13S,15Z,17S,18S,19R)-2,13,18-tris(2-amino-2-oxoethyl)-7,12,17-tris(3-amino-3-oxopropyl)-3,5,8,8,13,15,18,19-octamethyl-2,7,12,17-tetrahydro-1H-corrin-24-id-3-yl]propanoylamino]propan-2-yl] phosphate;cyanide | InChIKey | FDJOLVPMNUYSCM-WZHZPDAFSA-L |
| LogP | 3.409 | Topological polar surface area | 488.71 |
| Hydrogen bond acceptor | 20 | Hydrogen bond donor | 9 |
Synonym(s): vitamin B12; cyanocobalamin; 68-19-9; Vitamin B12 (charged); Cyanocobalamine; Cyanocob(III)alamin; Vitamin B12 complex; DSSTox_CID_24346; DSSTox_RID_80159; DSSTox_GSID_44346; Cobalamin (1+); MFCD00151092; C63H88CoN14O14P; CAS-68-19-9; NCGC00016302-01; Prestwick_564; Vitamin B12 NOS; DTXSID7044346; HMS1569G08; HMS2096G08; HMS3713G08; Tox21_110358; Tox21_113664; AKOS015894306; AKOS037515760; CCG-220433; DB00115; NCGC00249888-01; H486; V0344; 13408-78-1; Q55167869; Cobinamide,dihydrogenphosphate(ester),inner salt,3'-ester with(5,6-Dimethyl-1-a-d-ribofuranosyl-1H-benzimidazole-kn3),ion(1+)(9ci)
Activity data
|
No relevant experimental diagram |
Interaction ID | 622 |
| Target type | Molecule | |
| Target unique ID | 5311498 | |
| Activity | 88 nM | |
| Binding Conditions/Buffer | 1 M LiCl, 5 mM MgC12, and 25 mM HEPES (pH 7.4) or 1 M NaCl, 5 mM MgC12, and 25 mM HEPES (pH 7.4) |
|
| Assay | N/A |
|
| PubMed ID | 7508262 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_293 | RNA | CGGCCACAGAAUGAAAAACCUCAUCGAUGUUGCAUAGUUG | |
| Apta_521 | RNA | GGGUUGGGAAGAAACUGUGGCACUUCGGUGCCAGCAACCC | |
| Apta_374 | RNA | GUCCCGUGCGCAAAAGUUCUUAGCGCUAGCAGUCCUAGUUGC | |
| Apta_85 | RNA | UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA | |
| Apta_159 | DNA | GCGTGCAGCATGACCACCGATGTCACACTTAATGAGAAT | |
| Apta_4 | DNA | CCTGCCTTTGGAACCGACCGCCAGGCCGAGGAAAGGCACCGACAGC | |
| Apta_160 | DNA | CGGTGCAGTGGATACATGCCAGCCGTAGCCATCGTGGATA | |
| Apta_303 | RNA | CCUCCGGCUCAUACCUUUUCGAAGACAAGCUUCGACAGGAGG | |
| Apta_313 | RNA | UGCCCUGCCCUCACCCGUUAGCCUGAGCGCCCCGCA | |
| Apta_599 | RNA | GUCUCUGUGUGCGCCAGAGAACACUGGGGCAGAUAUGGGCCAGCACAGAAUGAGGCCC | |
| Apta_946 | DNA | TACCGGGTAATATGCACACATGCTGATAGCAAGCAATGCA | |
| Apta_599 | RNA | GUCUCUGUGUGCGCCAGAGAACACUGGGGCAGAUAUGGGCCAGCACAGAAUGAGGCCC | |
| Apta_447 | RNA | ACGCUCAACGAGCCAGGAACAUCGACGUCAGCAAACGCGAGCGCAACCAGUAACACC | |
| Apta_153 | RNA | CCACAGUUCAGAGGCACCGCGAACAAAACGCAAGACAGAGUGCCGACAAGAAC | |
| Apta_154 | RNA | ACACGCGAGAUAGAGCGAGGCCUCCAAAAAUGGCCACGCCAGGAAGCAAGU | |
| Apta_271 | RNA | CUGUCGAGCAUGCUCAGGGUAACGUAUAGUCAAGACACCUCAAGUGUAACU | |
| Apta_1143 | RNA | ACGAGUUGUCGCAUGUGCGGUUCAGUCUGGUCCUUCAGCACCGUACAACAA | |
| Apta_1121 | RNA | GACAGCGUGCCUAGAAGUCCAAGCUUAAAUAACCACGCUCGACAAGC | |
| Apta_1123 | RNA | AUUCGGGCCCAGGAACCAACUAUAUAAAUGUCCCGAAUGCUUCGACG | |
| Apta_86 | RNA | GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU |
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